Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

  1. Suresh V. Kuchipudi
  2. Meera Surendran-Nair
  3. Rachel M. Ruden
  4. Michele Yon
  5. Ruth H. Nissly
  6. Kurt J. Vandegrift
  7. Rahul K. Nelli
  8. Lingling Li
  9. Bhushan M. Jayarao
  10. Costas D. Maranas
  11. Nicole Levine
  12. Katriina Willgert
  13. Andrew J. K. Conlan
  14. Randall J. Olsen
  15. James J. Davis
  16. James M. Musser
  17. Peter J. Hudson
  18. Vivek Kapur

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Abstract

The results provide strong evidence of extensive SARS-CoV-2 infection of white-tailed deer, a free-living wild animal species with widespread distribution across North, Central, and South America. The analysis shows infection of deer resulted from multiple spillovers from humans, followed by efficient deer-to-deer transmission. The discovery of widespread infection of white-tailed deer indicates their establishment as potential reservoir hosts for SARS-CoV-2, a finding with important implications for the ecology, long-term persistence, and evolution of the virus, including the potential for spillback to humans.

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  1. Version published to 10.1073/pnas.2121644119
  2. ScreenIT

    SciScore for 10.1101/2021.10.31.466677: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    employed BioMek i7 liquid handling workstations (Beckman Coulter Life Sciences, Indianapolis, IN) and MANTIS automated liquid handlers (FORMULATRIX, Bedford, MA)
    BioMek
    suggested: (BioMek NXp NXp, RRID:SCR_019720)
    ; samtools version 1.11 (http://www.htslib.org, last accessed October 27, 2021) for sequence and file manipulation(34); and iVar version 1.2.2 (https://github.com/andersen-lab/ivar/releases, last accessed October 29, 2021) for primer trimming and variant calling(35).
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    All SARS-CoV-2 consensus genomes are deposited in GISAID and raw reads submitted to NCBI’s Short Read Archive (BioProject Number: PRJNA776532)
    Short Read Archive
    suggested: None
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Study limitations: The study has several limitations: The RPLN samples tested were from only one State in the USA, and the sampling was not uniform within the State. However, while the generalizability of our findings remains to be tested, we see no reason why this scenario has also not already played out in other regions with large deer populations with opportunities for contact with humans. Another limitation of our study was that RPLN samples tested were all from 2020 and early 2021, representing the early part of the pandemic before the global dissemination of the highly successful Alpha and Delta variants. Hence, surveillance efforts with robust longitudinal sampling approaches are urgently needed to determine whether deer will become long-term reservoirs for SARS-CoV-2 and potentially assume a role as generators of novel variant viruses that may repeatedly re-emerge in humans or spillover to other animal hosts. Concluding comments: To help predict or prevent the emergence of the next pandemic and control infectious diseases with pandemic and panzootic potential, a better understanding of the human–animal molecular and ecological interface and its relevance to infection transmission dynamics is essential (9). Thus, we call for an urgent need to implement a more proactive and robust “One Health” approach to better understand the ecology and evolution of SARS-CoV-2 in deer and other free-living species.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.10.31.466677v2 on bioRxiv
  4. Version published to 10.1101/2021.10.31.466677v1 on bioRxiv